Data representation

Spectra

class MSMetaEnhancer.libs.data.Spectra.Spectra

Bases: Data

Spectra class represents a single spectra dataset as a list. It is using matchms package to load and save MSP files.

fuse_metadata(metadata)

Fuse updated metadata back to its original format.

Parameters:

metadata

get_metadata()

Returns a list of dictionaries containing metadata for annotation.

Returns:

metadata in form of list of dictionaries

load_data(filename: str, file_format: str)

Loads given file as a list of matchms.Spectra objects.

Supported formats: msp, mgf, json

Parameters:

  • filename – given file

  • file_format – format of the input file

save_data(filename: str, file_format: str)

Exports all matchms.Spectra objects stored in self.spectrums to a file given by filename

Supported formats: msp, mgf, json

Parameters:

  • filename – target file

  • file_format – format of the output file

MSMetaEnhancer.libs.data.Spectra.spectra_eq(first: Spectrum, second: Spectrum)

Compare two Spectra objects. Native __eq__ definition does not work properly.

Parameters:

  • first – spectra object

  • second – spectra object

DataFrame

class MSMetaEnhancer.libs.data.DataFrame.DataFrame

Bases: Data

fuse_metadata(metadata_list)

Fuse updated metadata back to its original format.

Parameters:

metadata

get_metadata()

Returns a list of dictionaries containing metadata for annotation.

Returns:

metadata in form of list of dictionaries

load_data(filename: str, file_format: str)

Loads given file as a list of pandas DataFrame.

Supported formats: csv, tsv/tabular, xlsx

Parameters:

  • filename – given file

  • file_format – format of the input file

save_data(filename: str, file_format: str)

Exports DataFrame stored a file given by filename

Supported formats: csv, tsv, xlsx

Parameters:

  • filename – target file

  • file_format – format of the output file

General Data class

class MSMetaEnhancer.libs.data.Data.Data

Bases: ABC

General class for data.

fuse_metadata(metadata: List[Dict])

Fuse updated metadata back to its original format.

Parameters:

metadata

abstract get_metadata() → List[Dict]

Returns a list of dictionaries containing metadata for annotation.

Returns:

metadata in form of list of dictionaries